Assassin's Creed: Uprising
by Victoria-BlackHeart
Summary: Desmond didn't die when he released Juno. Five years later, he wakes up, with a limited memory of previous events, and finds out the Templars have overthrown the government and have been experiment with the pieces of Eden. Joined by previous and present Assassins, they must hurry to destroy the machine created, and whoever 'The Doctor' is.
1. Prologue: The Escape

_I'm dead._

That was the only thought he had in his mind.

_I'm dead. When I open my eyes, there will be nothing but white._

Slowly, he opened his eyes.

Darkness. He blinked a few times, his eyes trying to adjust. He sat up, and looked around. It was hard to tell where he was, or even what time of day it was. He reached his hands out blindly in front of him, feeling for any surface at all. His hands made contact with a hard surface, and he began feeling his way along it, hoping that it would lead him somewhere with light.

The only he heard was his breathing. Everything was silent. His hands hit something round, and he began feeling it. It felt like a door knob. _Where am I?_ he thought, and turned it, hearing the click that it was indeed a door. He pushed it open with his hands, and light flooded in.

He covered his eyes, stepping out into the light and looked around. He was in a hospital. He looked down and saw he was in normal clothes. Funny, he expected a hospital gown.

"WHERE IS HE?!"

He jumped, and turned around. The voice came from back in the darkness, echoing in the abyss. He felt a hand on his shoulder, and turned around.

"Good, it's you," He recognized the person, but they were dressed differently, "We need to get out of here before they find you," the person said, and turned around, "I know a way out. Follow me."

"Wait," he said, and the person turned around, "I know you."

"Of course you do. We've worked together side by side for the past five years. What did that doctor do to you?" he asked, walking over, "Do you remember my name?" He shut his eyes, trying to rack his brain.

"Shaun," he finally said, and Shaun smiled.

"So he didn't get to you, that's good," Shaun said, "Come on, follow me," Shaun began running down a hall, so he had no choice but to follow him.

"Wait how am I alive?" he asked.

"i was going to ask you the same question," Shaun answered, and stopped, leaning around the corner. He finally got a good look at Shaun, and saw it was not the same Shaun he knew. This one had war paint on his face, black clothes, and no glasses, "We all thought you were a goner like the others, but Lucy said you managed to contact her."

_Lucy?_ "The others?" Shaun looked at him.

"I'll explain everything once we get out of this god awful place," he said, "Come on, follow me," Shaun sprinted down the hallway, and he followed close behind.

"OI! GET BACK HERE!" He looked over his shoulder, and saw a group of men behind them, each holding machine guns.

"Come on we're almost there!" Shaun yelled, and pulled him down a different hallway just a spray of bullets was unleashed. They sprinted down the hall, but he saw they were coming to a dead end.

"There's no way out!" he yelled.

"Oh yes there is," Shaun said, and pointed to the window, "Get ready!" The men came around the corner, their boots thumping against the floor. Shaun grabbed his wrist, and jumped through the window, the glass shattering around them as they fell through the air. He felt the wind rushing by him, and wondered if he was going to hit the ground. He braced himself for impact.

It never came.

He opened his eyes, and saw they were on the wing of an airplane. Shaun held out his hand, "Come on, let's go," he said, and helped him up. The two climbed down the wings, and Shaun knocked on the cargo hold of the airplane. It slowly opened, and the two jumped in. Shaun stood up, brushing himself off, and turned to face him, "Do you remember your name?" Shaun asked.

"Uh...maybe," he answered, and Shaun stayed silent. They heard footsteps, and a woman appeared.

"Thank god," she breathed, and ran towards him, "I was so worried," she threw her arms around him, hugging him. He hugged her back.

"Lucy?" he asked, and she pulled back, nodding and smiling.

"You remember me, that's good," she took hold of his hands, "I was so relieved when you contacted me. We thought that you had died," He looked at her with a confused look, "You...you don't remember?" she asked, and he shook his head.

"We have a lot of explaining to do," Shaun said, and they walked back to the cockpit of the airplane.

There were two people in the cockpit, one in the pilot's seat and the other in the co-pilot. The pilot leaned around, "That was quite an escape," he said, as the three people took their seats, "How much does he remember?" he asked, looking at Lucy.

"He knows who me and Shaun are," she answered, and the pilot frowned.

"He doesn't look like the others. Maybe the doctor didn't get to him."

"Doctor? What doctor? What is going on?" he asked, looking around.

"Do you remember who you are?" Lucy asked, and he shut his eyes, trying to remember.

_"What do they want with me? With us?"_

_"I don't know. But you need to find a way out Des."_

He opened his eyes, "Des," he whispered, "My name is Desmond."

"That's a relief," the co-pilot said. Lucy looked at him.

"What do you remember?" Lucy asked, and Desmond frowned.

"There was a woman with me, but...I don't remember who she was. She said I needed to find a way out," He placed his hand against his head, "Why can't I remember anything?"

"It must be something the doctor did to you," the pilot said, "And since you don't remember who I am, name's Leonardo, and this is my co-pilot, Rebecca," Rebecca leaned around and smiled.

"I remember you. Both of you...but...how are you here Leonardo?" he asked, and Leonardo frowned.

"The same way you are. My mother gave birth to me," he answered.

"Leave him alone Leo," Lucy said, and placed an arm around Desmond, "He's tired. Get some rest, we'll explain everything when we get back to base," she said, and Desmond got up, heading back into the cargo hold.

* * *

_Oh no! What has happened to Desmond? Where is he now? Tune it to find out!_


	2. Chapter One: Don't Ask Questions

_"What do you want with me?!" he yelled, as the two men dragged him through the hallway. He saw other people, staring out through the bars, their eyes blank._

_"Isn't it obvious?" he heard that familiar voice, and was thrown into a room, "To erase all your memories."_

_"You're fucking sick," he spat, and the Doctor simply chuckled._

_"I've been called a lot worse."_

Desmond opened his eyes, and sat up, slowly. The room around him was spinning. He closed his eyes, trying to focus on what was around him, "Desmond?" He opened them, and saw Lucy, "We've landed," she said, and Desmond nodded. He carefully stood up, but was having trouble keeping his balance. Lucy rushed over, and put one of his arms around her, "Hey, you feeling ok?" she asked, and Desmond looked at her arm.

"Yeah," he mumbled. _This has to be a dream. You're dead, _he thought, as they made their way to the front of the airplane.

They were inside of a hangar, and they had the same set up that they had in the villa back in Italy. Desmond looked around, and he saw that everyone had stopped what they were doing. They all looked at him, "Why are they looking at me?" he asked.

"They all thought you were dead," Lucy answered, as she led him up a set of stairs.

"I'm supposed to be," he mumbled, and she led him to a room at the back.

Lucy pushed open the door, and an older gentlemen turned around. His eyes went wide when he saw Desmond, "Not possible," he whispered, "You found him," Lucy helped Desmond down into a chair, and walked over to the man, "Where?"

"At the hospital," she answered, and took a bottle of water. She opened it and walked back over to Desmond, handing it to him, "Here drink," she said. Desmond took it, and drank most it, "He doesn't have most of his memory," she explained, "We're going to have to help him remember certain things," The older man looked at Desmond.

"He doesn't remember who I am, I can see it in his eyes," he said, and he walked over to Desmond, "Desmond, do you know who I am?" Desmond looked at him, and shook his head slowly, "It's me. Your father. William Miles, or Bill. Do you remember?" Desmond shut his eyes, trying to remember the name and the face.

"I...remember...that name..." he said, his eyes shut. Lucy looked at Bill, who sighed, "That's all."

"It will take some time," Bill said, and Rebecca rushed into the room.

"Hey they're back," she said, and Lucy followed her downstairs. Desmond got up, and looked over at Bill.

"You're my father," he said, and Bill nodded. Bill walked over to his desk, and picked up a picture frame. He walked over to Desmond and handed it to him. Desmond looked down at it, and saw himself, Bill and Lucy. Lucy was wearing a white dress while himself and Bill were wearing tuxedos.

"When was this taken?" Desmond asked, and Bill took it back from him.

"Your wedding," he answered, "Yours and Lucy's wedding," Desmond's eyes went wide.

"We're married?" he asked, and Bil nodded.

"Hey Bill! We got some more info!" Bill walked by him, and patted him on the shoulder..

"We'll talk later son," he said, and walked down the stairs, leaving Desmond alone in the room.

Downstairs, Shaun was busy helping two people sort through files while Leonardo was bandaging up a third person, "Well?" Bill asked, as he stopped midway down the stairs, "Anything?"

"We found a map that will lead us to them, but we didn't actually find any of them," one of the men said. Bill sighed, and continued walking down the stairs, "What's this I hear about Des being alive?"

"He's alive Connor, but...his memory..." Connor looked at him.

"The Doctor got to him," he said.

"Not exactly," Shaun cut in, "He remembers some things, like certain people and stuff like that, but other than that he has no memory of anything," Connor looked over at the second man looking at the maps, "What are you thinking Connor?"

"He might be able to help Altaïr," Connor said, and the second man looked up.

"It's a possibility," he said.

"Come on Malik, it's worth a shot," Connor said, and looked over at Leonardo, "Ezio?"

Ezio grimaced as Leonardo finished stitching his wound up, "Yeah totally. Altaïr doesn't even remember who we are. All he does is sit in that damn chair and stare out the window all day. What does he look at anyways?" He pulled his arm away, "That frigging hurts!" he snapped. None of them noticed Desmond at the top of the stairs.

"Where's Altaïr?"

Everyone turned around, and they saw him there. Connor looked at Malik, "Follow me," Malik said, and turned to walk down a hall, Desmond behind him.

They walked in silence until Malik stopped at a door, and he quietly opened it. The room had shelves of books, a desk in the middle, and a few lamps lit. Malik pointed to the lower level, and Desmond saw Altaïr sitting in a chair, his back turned to them. He wasn't moving, just looking out the window, "What happened?" Desmond asked.

"The Doctor. He did the same thing he's done to everyone. It's how he tried to control them. Wipe their memory clean and fill it with new thoughts. Only...he didn't get a chance to do that with Altaïr. We got to him before that, but...he didn't know who any of us were."

"What about now?"

"He knows who I am, but no one else. He also keeps bringing up this Maria person, whoever that is."

_"What's your name?"_

_"I...I'm not sure I remember," She placed a hand on his shoulder._

_"My name is Maria."_

"I know her," Desmond said, "I remember her."

"It can't be the same one," Malik said.

"There was a Maria at the hospital but...I don't know," Desmond said, "I don't understand what is going on. I'm supposed to be dead," Malik was silent, then he spoke.

"I know."

Desmond turned and looked at him, "We're all supposed to be dead. Me, Altaïr, Ezio, Connor. But...we're not," Malik never looked at Desmond while he spoke. Desmond looked at Altaïr, "We just...accept how things are, and don't ask questions. That part is important. The Templars don't like it when we ask too many questions. So, we keep our questions to ourselves, and we stay up all night, staring at the ceiling and wondering why," Malik shrugged, and turned and left, leaving Desmond alone.

"What the hell?" he asked, "I need to find out what's going on."

* * *

_Sorry if you guys are a bit confused but everything will explained in the next chapter and I'm a horrible person for not updating consistently I am so sorry._


	3. Chapter Two: The Truth Comes Out

Desmond quietly pushed open the study door, and looked around the dark room. He saw Altaïr's shape sitting in the same spot. He took a deep breath and walked over to him, "Altaïr, I need to ask you some questions since no one will answer them," Altaïr didn't answer, "Ok. I know you've had your memory wiped but could you at least acknowledge me?" Still no answer. Desmond frowned, and walked around him, and turned to face him, "What the hell?"

Altaïr had tape over his mouth, his hands and ankles were bound to the chair. Desmond pulled the chair off and Altaïr gasped for air, "I was wondering how long it was going to take you," he said, as Desmond behind cutting the rope. Once he was done, Altaïr stood up, rubbing his ankles. He glanced over his shoulder, then looked back at Desmond, "Push one of the bookcases in front of the door, then we'll talk," Desmond frowned, but did what he asked.

Once the bookcase was in front of the door, Desmond walked back over to Altaïr, "What is going? I don't understand anything."

"Of course you don't," Altaïr said, "You see, when you released Juno into the world, both the Assassins and the Templars were trying to stop her. The Templars made a deal with the government, in which the government promised to let them put some of their men in office. However, we all know the Templars are liars and want more than a few people in office. Unfortunately, the Templars found and destroyed Juno first. When they went to the government, they demanded that the president step down and let them take control. Of course he didn't, and everyone was killed. The Templars overthrew the government, and now control everything."

"They also have the Apple and a few more pieces of Eden. One of their men, known only by The Doctor, did some experimenting with them. He wanted to find a way to make people more obedient by creating a block on their mind. This block would erase all of their memories, and then the Templars could fill it with their own set of ideas. And it worked," Desmond was shocked. He leaned back against a wall, trying to process it, "For this next part you might want to sit down," Altaïr said, and pulled up a chair. Desmond sat down in the chair as Altaïr sat on the desk across from him, "That's not the worse part. Your dad? The Templars got him, and wiped his memory."

"That's not possible. He knew who I was," Desmond said.

"He knows so the Templars can find you. They tried to wipe your memory already, I overheard Bill and Malik talking about it. And Lucy and them? They had their memory wiped as well. The Templars control them. Except...the memory block isn't strong enough for the mind of an Assassin. That's why they have to go back every couple of weeks for The Doctor to operate on them," Desmond leaned forward, his head spinning.

"Why were you locked in here?" Desmond asked, looking up at Altaïr.

"Because I missed the last trip to get my memory wiped. All my memories-my _real _memories-came back, and I started asking questions. I started telling Malik about our past life, and he told Bill. So, Bill locked me up so I wouldn't make the others come back to the real world. They all live in a fantasy world. You and Lucy were never married, The Doctor implanted that memory in her brain," They heard a knock on the door. Desmond looked at the door.

"Who is it?" he asked.

"It's Rebecca. Your dad wants to see you," Altaïr looked at him.

"He's told the Templars where you are. They're here to bring you back to the hospital and wipe your memory," Altaïr said low, and Desmond got up, walking over to the door.

"I'll be there in a minute. Just...organizing the books," he said, and he heard Rebecca walk away.

"You're not safe here," Altaïr said, "We need to get out of here," Desmond looked at him, then heard pounding on the door.

"Desmond what are you doing in there?" he heard his father demand, "Why is the door locked?" Altaïr looked at him, and shook his head. Desmond didn't say anything and slowly backed away from the door, "Desmond what is going on in there?" Altaïr walked over to one of the windows. He ran his hand over the glass, then picked up his chair and threw it through, the glass shattering, "Desmond what did you just do?!"

"Open the door Des please!" he heard Lucy plead, then he heard thumping from the other side.

"They're trying to break through," Desmond said, as he ran over to where Altaïr was. Altaïr nodded, and looked out the window. He saw the water hit against the rocks, "We're not seriously going to jump, are we?"

"Unless you want them to catch you, we have to," Altaïr answered, and the bookcase fell against the floor as the swung open. Bill, Lucy, Rebecca, Malik and Ezio entered the room. Bill's eyes went wide.

"You! How dare you free him!" he yelled, "He tells lies!"

"No you're the one who tells the lies dad!" Desmond yelled back. Altaïr looked at them.

"You can't hide reality from them for much longer Bill," he said, and jumped out the window. Desmond looked over his shoulder, and saw Altaïr disappear into the water.

"If you jump out that window, you'll betray all of us," Bill warned, and Desmond glared at him.

"You've already betrayed me and them, so what difference does it make?" Desmond asked, and before he could hear Bill's response, Desmond followed Altaïr and jumped out the window, falling through the air, and plunging into the dark water.

Bill looked over, staring at the waves, "What do we do? The Doctor is going to be here any day," Malik asked.

"We need to find them. And when you do, bring back Desmond alive," Bill answered, and walked towards the door.

"And Altaïr?" Malik asked, and Bill stopped.

"Kill him."


	4. Chapter Three: The R Word

"Desmond wake up."

Desmond opened his eyes, and saw Altaïr leaning over him. He looked around, "Where...where are we?" he asked, his eyes adjusting to the darkness.

"We're safe, for now anyways, but we're going to need to move quickly," he answered, and Desmond sat up. He saw a blanket had been draped over him, "I hate to throw more information at you, but that girl that you think is Lucy, isn't her," Desmond frowned.

"What are you saying?" he asked, standing up. Altaïr looked around, his eyes scanning the area, "Altaïr."

"She is just someone who looks like her, and unfortunately, the Templars knew this. She had her memory wiped as well, so she thinks she's Lucy."

"So the real Lucy is dead," Desmond mumbled, and Altaïr looked over his shoulder at him.

"I'm sorry Desmond," he said, "Come on, we have to get moving."

* * *

They made their way onto the highway, and began walking down the long stretch of road, "Why can't we hitchhike?" Desmond asked, his breath visible against the cold air.

"Knowing your father, he probably has an alert out for us already. We can't risk it," Altaïr answered, shoving his hands in his pockets. Desmond looked around, squinting against the darkness.

"You picked a great night to go for a swim," he commented, and Altaïr chuckled.

"Not one of my better ideas, I'll admit," he said, "There's a gas station up ahead we can grab some food and stay warm for a bit."

They walked up to the gas station and Altaïr pushed the door open, the bell going off. The woman behind the counter looked up, and Desmond saw that her eyes were glazed over. Altaïr walked over to a booth and sat down, Desmond following him. The woman grabbed two menus and walked over to them. She placed them down, and pulled out a notepad, "Can I get you something to drink?" she asked.

"Coffee, for both of us," Altaïr answered, and she nodded, walking away. Desmond leaned forward.

"What's wrong with her eyes?" he asked low.

"That is what happens when the people are brainwashed," he answered, leaning back in the booth, "We have to be careful about what we say," The woman came back over and placed the coffee down, along with sugar and cream.

"What can I get you to eat?" she asked. Desmond opened the menu, and scanned it.

"I'll have the clubhouse and fries," Altaïr said, not even opening the menu. Desmond looked up, and saw her staring at him.

"I'll have the same," he said, and she took the menus, "What was that about?"

"They don't know any better," he answered, and looked up as the bell rang, "Shit," he muttered, and ducked his head. Desmond glanced over his shoulder, "Don't look," Desmond turned his head back to him, "Those two men who just walked in, they're part of a secret police the Templars have put together. They're on the look out for anyone who acts out of the ordinary, or who mention the 'r' word," Desmond frowned.

"'R' word?" he asked. Altaïr saw one of them look over, and he pulled out a pen, writing it on a napkin. He pushed it towards him.

**REVOLUTION**

Desmond took the napkin and put in his pocket. The woman brought their food over, "Enjoy," she said, and walked back to the counter where the two men were. Desmond picked up a fry, and took a bite.

"I'm starved," he said.

"Eat your food slow," Altaïr instructed, "They'll get suspicious," One of the police turned their heads towards them, looking at them. He frowned, and nudged his partner. Altaïr lowered his head, and slowly began eating. Desmond looked down at his plate.

_"What do they want with me Maria?" he asked, as she bandaged his wound. Maria looked up._

_"The same thing they want with everyone else," she answered, rinsing the cloth off, "You took a nasty beating," Desmond looked down at his wound._

_"Someone needs to stop them," he said._

_"People have tried, but they failed. Every revolution has failed...so far..."_

Desmond looked at Altaïr, "I'll be right back," he said, and got up, heading to the bathroom.

Desmond leaned against the sink, and looked up. The word revolution flashed whenever he shut his eyes. That's what they needed to do. They needed to start a revolution. Desmond stared at his reflection, then turned on the faucet. He splashed water onto his face, trying to clear his head. He turned it off, and looked up again.

**RAISE YOUR FLAG**

Desmond took a step back from the mirror, staring at those words. They hadn't been there before. He grabbed paper towel, and dried his hands, quickly leaving the restroom.

He sat back down, and picked at his food. Altaïr looked up, frowning.

"What's wrong?" he asked.

"Nothing," Desmond answered, and one of the police walked by them.

Moments later, he came out of the restroom and fired shots into the ceiling, "Which one of you traitors did it?" he yelled, "All of you, on the ground now!" he yelled, and everyone scrambled to the ground. Desmond and Altaïr did the same thing. Desmond's heart was beating. His partner looked at them, his eyes scanning everyone.

"Which one of you wrote that on the mirror?" his partner asked, as the first police began searching pockets. Desmond felt his heart speed up. They were going to find the napkin, "No sound, eh? We have ways of making you talk," he said, staring at them, "Hmm? No one?" The first one reached down and searched Desmond's pockets.

"Hang on, what do we have here?" he asked, pulling the napkin out. He unfolded it, "Got him," He grabbed Desmond by his arm and pulled him to his feet. Altaïr looked up. The first officer pushed Desmond onto a table, and held his gun at his face, "Now, what are you planning?" Desmond didn't say anything, "The silent type," He pulled out handcuffs and put them on Desmond, then led him outside. Altaïr slowly got up, and the second one turned around.

"You, back on the ground," Altaïr reached into his pocket, grabbing a throwing knife, "I said down on the gro..." Altaïr wiped the knife, hitting him square in the chest. The officer fell down, and he walked past him, heading outside.

Desmond looked over his shoulder, and he saw Altaïr, "Move it," the officer pushed him towards a car. Altaïr ran up silently and stabbed the police in the back with his hidden blade. The officer fell down, and Altaïr picked the lock on the cuffs.

"That was way too close," he said, "Get in the car."

"We're stealing it?" Desmond asked, and Altaïr nodded.

"There's no way we can make it to the city on foot without someone catching us. Let's go."


	5. Chapter Four: A Solid Plan

"What's our next move?" Desmond asked, as Altaïr pulled the car into an alley. He shut off the engine, and looked at him.

"This is going to sound crazy, but we have to go back and get Lucy look-a-like. I have a feeling she can help us."

"But..what about her memory?" Desmond was confused.

"Like I said before, the block on her memory doesn't last long. If we time it right, we can get to her before her next appointment with the Doctor," Altaïr explained, "There's...something about her."

"What about the Maria person?" Desmond asked, and Altaïr frowned.

"That name sounds familiar, but I don't know why," he said, "Anyways, we should get some sleep," Altaïr got out of the driver's seat and crawled in the back, "We'll take turns. Wake me in two hours," he said, and shut his eyes, resting his hand behind his hand.

Desmond leaned back in his seat, tapping his fingers on the dashboard. He breathed out, and looked around, taking in the dark alley. He wondered who that girl was. He felt his eyes starting to shut, so he sat up straight and shook his head, "Stay awake," he mumbled, but his eyes felt so heavy, "Stay...awake..."

_It was a warm night. The air was thick with the humidity. She walked towards her car, the bag on her arm swinging back and forth. Her cell phone rang, and she pulled it out, "Hello?"_

_"Where are you?" the male voice asked, concerned._

_"Sorry I got held up at the office. I'm on my way home now." she answered._

_"Alright. I'll see you in a bit," she hung up, and out the phone back in her purse. She pulled out her car keys, and unlocked the black car in the parking lot. She heard footsteps behind her, and looked over her should. There was no one there. She frowned, and turned back to her car. _

_There was two men standing by it._

_"Can I help you?" she asked._

_"Yes, you can," one of the men answered, taking a step towards her, "We need you to come with us," he said, and she saw the symbol on his arm. She took a step back, then turned and began running, the two men chasing her. _

_She sprinted down the street, hoping that a corner store would be open. She stopped and banged on the door, "Please open up!" she begged, pounding on the glass. A pair of arms wrapped themselves around her, pulling her back kicking and screaming, "Let me go!" she yelled, and the man stabbed a needle in her neck, injecting her. _

_Slowly, she stopped fighting, and became limp in his arms, "That turned out to be harder than I thought," the second man said, as a van pulled up besides them, "Quick, get her in."_

"Desmond."

Desmond's eyes snapped open, and saw Altaïr's face leaning over him, "You didn't wake me," he said, and Desmond blinked a few times.

"Sorry," he mumbled, and looked around. They were still parked in the alley, "What time is it?"

"It's five am," Altaïr said, and Desmond rubbed his eyes, "You looked like you were having a nightmare. Is everything ok?"

"Yeah everything's fine," Desmond answered, as Altaïr started up the car, "So, what's the plan?"

"We head back, and find Lucy look a like," Altaïr answered, "And kill anyone who gets in our way."

"Sounds like a good plan to me," Desmond said, and Altaïr tore out of the alley.


End file.
